The Sequence view displays the amino acid or nucleotide sequence, secondary structures, binding sites, disulfide bonds, and a ruler. Colorful graphics denote features derived from annotations in the structure file.
By default, the Sequence view is shown vertically in the middle of the Protean 3D window. If the Sequence view is hidden or absent, you can display it using View > Sequence > Show. Alternatively, you can reset the entire Protean 3D window to the default layout using View > Document Layout > Restore DNASTAR Default Layout.
Selections within this view are synchronized with other views in Protean 3D. Similarly, selections made elsewhere will be highlighted simultaneously in the Sequence view.
Descriptions of graphics in the Sequence view:
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Protein sequence residues and the ruler. |
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Structural gaps are displayed as grayed-out residues. If a structural gap comprises an entire row, no ruler will appear under it, since PDB files do not contain numbering information for gaps. A ruler is shown, however, if the gap occurs in the same row as regular sequence. In this case, the number to the right of the ruler for that row shows the position of the last residue before the gap. |
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Helical structure. |
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Site. |
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Beta sheet secondary structure. |
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Site hubs use the site identifier listed in the PDB file. This 3-letter code is the same one that is used in the Style. The lines between hubs indicate the locations where bonds occur. |
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Disulfide bond residues. |
Tasks that pertain to the Sequence view:
| Task | How To |
|---|---|
| To change the font style or size | Use the Font menu in the Sequence section. |
| To change the order of rows | Click+drag* the row label (e.g. Sequence, KDS 2°, Sites, Ruler) to the desired position. |
| To create a new feature | Select the range for the feature, then right-click on the selection and choose New Feature. |
| To control the display of features | Use the checkboxes in the feature Style sectionto toggle between showing and hiding features. Selections may be made for individual features or for entire feature classes. |
| To delete a feature | Right-click in the feature and choose Delete Feature. |
| To make selections in the view | See Make a Selection. To select everything except the current range, right-click on the selection and choose Invert Selection. |
| To copy a selection from the view | Right-click on the selection and choose Copy. |
| To create a virtual mutation within the current selection | Right-click on the selection and choose Create Variants. The Protein Design wizard opens with the Substitutes screen already populated for the selected range. |
| To change the layout of the view or what is displayed in it | See Customize the look and layout. |
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